From: Axel Kohlmeyer (
Date: Wed Oct 22 2008 - 10:38:15 CDT

On Wed, 22 Oct 2008, Tomek Wlodarski wrote:

TW> Dear Axel,
TW> thanks for reply!
TW> You are right that averaging structures should give the same result
TW> like averaging density map.
TW> But I wanted not to average density maps- only add them, and after
TW> that try to fit rigid structure.

TW> So for example for all observed rotamers I would not get average
TW> density of rotamers (which would be some kind of fuzzy cloud) but
TW> density map representing all rotamers (calculate density map for each
TW> rotamer, after superimposing, and add this maps). Then to this density
TW> map representing all conformation I would like to try fit rigid
TW> structure.

but that would sill result in practocallythe same fit. the difference
between the two density maps is simply a scaling factor, since the
density in the rotation center would be multiple times higher. even
if you don't use addition to combine the grids but use a MAX() operation,
your fit to the density would be as bad as the fit to an average structure.


TW> Best,
TW> tomek

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.